Open Access Research article

Inferring the relation between transcriptional and posttranscriptional regulation from expression compendia

Ivan Ishchukov1, Yan Wu1, Sandra Van Puyvelde1, Jos Vanderleyden1 and Kathleen Marchal123*

Author Affiliations

1 Center of Microbial and Plant Genetics, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium

2 Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium

3 Department of Information Technology, Ghent University, IMinds, VIB, 9052 Gent, Belgium

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BMC Microbiology 2014, 14:14  doi:10.1186/1471-2180-14-14

Published: 27 January 2014



Publicly available expression compendia that measure both mRNAs and sRNAs provide a promising resource to simultaneously infer the transcriptional and the posttranscriptional network. To maximally exploit the information contained in such compendia, we propose an analysis flow that combines publicly available expression compendia and sequence-based predictions to infer novel sRNA-target interactions and to reconstruct the relation between the sRNA and the transcriptional network.


We relied on module inference to construct modules of coexpressed genes (sRNAs). TFs and sRNAs were assigned to these modules using the state-of-the-art inference techniques LeMoNe and Context Likelihood of Relatedness (CLR). Combining these expressions with sequence-based sRNA-target interactions allowed us to predict 30 novel sRNA-target interactions comprising 14 sRNAs. Our results highlight the role of the posttranscriptional network in finetuning the transcriptional regulation, e.g. by intra-operonic regulation.


In this work we show how strategies that combine expression information with sequence-based predictions can help unveiling the intricate interaction between the transcriptional and the posttranscriptional network in prokaryotic model systems.

sRNA; Gene; Module network; Network inference; Escherichia coli